Background:

• NIH Pathway to Independence Grant (K99/R00), 2007 – present
• American Cancer Society Postdoctoral Fellow, The Scripps Research Institute, 2006 – 2007
• Ralph F. Hirshmann - Daniel H. Rich Graduate Award in Bio-organic Chemistry, UW – Madison, 2005
• NIH Predoctoral Fellow, Biotechnology Training Program, 2001 – 2004

Research in the Carlson laboratory will utilize a combination of chemical tools to both define the mechanisms of bacterial pathogenesis and identify potential therapeutic agents. I nfectious diseases are the second-leading cause of death worldwide and the third-leading cause of mortality in economically advanced countries. Despite early optimism following the discovery of antibiotics, it is now apparent that bacteria are continually evolving resistance. New tools are therefore needed to increase our understanding of bacterial pathogenesis and to discover new antibiotic agents. My research program will develop and apply advanced chemical biology and systems biology technologies to that end through pursuit of two avenues of investigation: (1) development and application of technologies for natural product discovery including innovative methods for compound isolation and screening, and (2) characterization and targeting of bacterial pathogenesis and antibiotic resistance through biochemical pathway discovery facilitated by global molecular profiling (i.e., metabolomics and proteomics). Projects in my research group will be highly multidisciplinary and members will gain expertise in organic synthesis, chromatography, mass spectrometry, structure elucidation, proteomics, metabolomics, biochemistry, microbiology, and molecular biology.

Development of a novel method for discovery of bioactive natural products.

 

Figure 1. Structures of a variety of natural products displaying functionalities common within nature's small molecules.

Since the dawn of medicine, compounds derived from natural sources have been used as therapeutic agents (Figure 1). In fact, more than 75% of treatments for infectious disease have been developed from natural products. The continued exploration of the small molecule repertoire of many organisms, such as plants and microbes, is bound to prove fruitful for the discovery of novel bioactive compounds. However, a major roadblock to the identification of pharmacologically active natural products is purification, as they are generally present as minor components of biological extracts. Current strategies facilitate enrichment based on a restricted set of separation mechanisms that are dependent upon physical properties such as solubility or size. To produce a separation strategy that provides a significant improvement over existing techniques, a method that employs enrichment principles that are independent of physicochemical properties must be devised. Accordingly, my research group will develop an innovative technology that separates natural products based upon a distinct and orthogonal chemical property: functional group composition.

Figure 2. Depiction of the general natural products enrichment strategy. A complex mixture of compounds is subjected to a RET that will selectively enrich one functional group class (green). The resin is washed to remove natural products not displaying this functional group. The enriched compounds are then released.

To accomplish this goal we will develop a reversible tagging strategy that will covalently capture small molecules, enabling their selective enrichment, followed by release of the unaltered chemical structures. We will apply a suite of “capture and release” tags, called reversible enrichment tags (RETs), to purify specific classes of natural products from complex biological preparations (Figure 2). Following enrichment, compounds will be liberated using conditions that will not interfere with subsequent bioassays. This method will allow us to explore and harness the immense diversity of nature’s molecular repertoire with unprecedented scope and depth. The RET method will be employed to identify novel bioactive natural products, focusing on discovery of compounds with antimicrobial activity from microbes and plants.

Assembly of biochemical networks that contribute to bacterial pathogenesis.

With the advent of the “age of antibiotics” in the 1940s, many believed that we had conquered these dangerous microbes. However, it quickly became apparent that the ability of bacteria to evolve resistance had been sorely underestimated. My research group will utilize an integrated molecular profiling system, including innovative metabolomic and functional proteomic methods, to construct a list of biochemical pathways whose function may be important for disease pathogenesis and the development of new antibiotics (Figure 3).

Figure 3. Overview of global molecular profiling methods. We will utilize my METPR technology, in conjunction with functional proteomic and genomic methods, to identify the enzymes, metabolites, and biochemical pathways involved in bacterial pathogenesis.

To identify metabolites associated with bacterial pathogenesis, we will employ the metabolomics profiling technology developed in my postdoctoral tenure (Metabolite Enrichment by Tagging and Proteolytic Release or METPR). This method utilizes chemical tags to facilitate the enrichment of many classes of metabolites. To identify enzymes that play key metabolic roles in pathogenesis, we will conduct a functional proteomic analysis of enzyme activities using activity-based protein profiling (ABPP). ABPP utilizes active site-directed probes to selectively label active enzymes, but not their inactive forms, facilitating the characterization of changes in enzyme activity that occur without alterations in protein or transcript expression. The information garnered from these studies will be integrated with genomic data. Validated hits will provide a crucial starting point for development of a more comprehensive understanding of bacterial pathogenesis and could provide novel therapeutic targets.

Selected Publications:

1. Carlson, E. E. and Cravatt, B. F. Enrichment Tags for Enhanced-Resolution Profiling of Hydrophilic Metabolites. J. Am. Chem. Soc. 2007 , 129, 15780-15782.

2. Carlson, E. E. and Cravatt, B. F. Chemoselective Probes for Metabolite Enrichment and Profiling. Nat. Methods, 2007 , 4, 429-435.

3. Carlson, E. E.; May, J. F.; Kiessling, L. L. Chemical Probes of UDP-Galactopyranose Mutase. Chem. Biol.2006, 13, 825-837.

4. Soltero-Higgin, M.; Carlson E. E.; Phillips, J. H.; Kiessling, L. L. Identification of Inhibitors for UDP-Galactopyranose Mutase. J. Am. Chem. Soc. 2004, 126, 10532-10533.

5. Soltero-Higgin, M.; Carlson, E. E.; Gruber, T. D.; Kiessling, L. L. A Unique Catalytic Mechanism for UDP-Galactopyranose Mutase. Nat. Struc. Mol. Biol. 2004, 11, 539-543.

6. Carlson, E. E. and Kiessling, L. L. Improved Chemical Syntheses of 1- and 5-Deazariboflavin. J. Org. Chem. 2004, 69, 2614-2617.